MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Ontology Breakdown

Below is a table that can help you break down the effect of the gene alteration on the bioloigcal system. To create the table below we went over all the ontology terms and counted the number of times a gene was listed in that specific class, or one of its children. As can be expected, each class will differ in its behavior. Some will have a strong average regulation, but will contain very few genes, while others will be very large and broad classes that will have a lower average regulation, but which will whos an overall effect with many genes in many subgroups being affected.

The best strategy to analyze such classes is to a) filter out all the classes for which we have too little data (less than 5 affected genes on the micro array measurement). This can be done by writing '>5' in the 'Affected Genes' field. SEcondly we might also want to look at one specific ontology at first (click on 'biological process' in the table.

Once this is done we can sort the data properly by placing the 'Average Regulation' to the left (click on the green arrows) and the '% Affected Genes' as a second. We also want to sort them descending (the grey arrow should be pointing downward).

Now we can go investigate the data by first look at broadly affected classes ('Would Be Affected Genes'>60) and progressively lowering this value (to something like 'Would Be Affected Genes'>20)

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Would Be Affected (#genes)	% Affected Genes	Class	Class Size (#genes)	affected	Microarray Measured (#genes)	Average Regulation (ratio)	Class	Accession

Results: HTML CSV LaTeX

Showing element 1 to 50 of 173 in total

Class  : biological process

Would Be Affected (#genes)	% Affected Genes	Class	Class Size (#genes)	Average Regulation (ratio)
6	5.1546	embryonic morphogenesis	107	2.329086923599243
	3.3333	regulation of cell differentiation	170	1.3052469968795777
	2.9412	chromatin modification	195	2.9956377029418944
	2.9070	nucleocytoplasmic transport	206	2.844642996788025
	2.8249	visual perception	211	2.7829527854919434
	2.8090	sensory perception of light stimulus	212
	2.7174	microtubule-based process	231	3.0316067695617677
	2.6596	anion transport	229	1.6556044340133667
	2.4510	regulation of protein kinase activity	236	1.7727066993713378
	2.3810	regulation of kinase activity	243
	2.3585	positive regulation of apoptosis	250	1.4007941484451294
	2.3364	mRNA processing	242	1.7531960964202882
		positive regulation of programmed cell death	252	1.4007941484451294
		regulation of transferase activity	247	1.7727066993713378
	2.2321	chemical homeostasis	260	1.368695902824402
	2.1930	cell-cell adhesion	287	1.8477724552154542
	2.1368	lipid biosynthetic process	275	1.7971266508102417
	2.0661	positive regulation of cell proliferation	272	1.9144784212112427
	2.0492	regulation of developmental process	276	1.3052469968795777
	2.0161	potassium ion transport	292	2.4153901100158692
	1.9841	mRNA metabolic process	289	1.7531960964202882
	1.8727	amino acid metabolic process	314	1.575242853164673
	1.8051	negative regulation of transcription	325	2.4346015453338623
	1.4970	behavior	398	2.3127479553222656
	1.1390	carbohydrate metabolic process	544	2.745920252799988
	1.0870	cellular catabolic process	559	1.9687834978103638
	0.8741	catabolic process	704
7	5.7692	muscle development	117	2.6894871592521667
	4.7244	mitosis	142	1.632481078306834
	3.9735	transmembrane receptor protein tyrosine kinase signaling pathway	164	2.267966568470001
	3.0303	cell division	222	1.3425244291623433
	2.0833	protein complex assembly	335	1.9949067831039429
	2.0202	response to DNA damage stimulus	337	1.6523104111353557
	1.9608	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	358	2.2540424267450967
	1.8293	amino acid and derivative metabolic process	388	1.5113894144694011
	1.5228	monovalent inorganic cation transport	464	2.2601398825645447
	1.4634	regulation of catalytic activity	501	1.683560033639272
8	3.9773	regulation of growth	192	2.6829177481787547
	3.7234	RNA splicing	208	1.8230999537876673
	3.4146	cell cycle phase	229	1.6467143297195435
	2.5271	nervous system development	321	2.2348088707242693
	1.9608	negative regulation of cellular metabolic process	414	2.2326475211552212
	1.8421	response to endogenous stimulus	428	2.158773183822632
	1.7949	amine metabolic process	463	1.5929162161690849
	1.7157	nitrogen compound metabolic process	484
	1.6092	regulation of a molecular function	527	1.6290612050465174
	1.5748	electron transport	514	1.4910563230514526
9	6.3492	protein amino acid dephosphorylation	142	2.1655175536870956
	5.7143	dephosphorylation	158
	3.8095	enzyme linked receptor protein signaling pathway	230	2.3925783783197403

Legend:
- The Average Regulation (ratio) is calculated only for the measured genes in this gene ontology term
- % Affected Genes is the % of genes in this gene ontology class that have been affected by the Mk5 alteration.
- Would Be Affected (#genes) represents how many genes of the overall class would have been affected if we measured each of them.
- The Class Size (#genes) counts the number of genes listed under the specific gene ontology term.
- Class is the GO class description.
- The Class refers to the ontology category, which can be molecular_function, biological_process or cellular_component.
- The Microarray Measured (#genes) lists how many genes of the specific ontology term were measured.
- Accession is the GO accession key.